Summary: OB-fold nucleic acid binding domain
OB-fold nucleic acid binding domain Provide feedback
This family contains OB-fold domains that bind to nucleic acids . The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D; , Science 1991;252:1682-1689.: Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). PUBMED:2047877 EPMC:2047877
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004365
The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates.
This entry contains OB-fold domains that bind to nucleic acids [PUBMED:10829230]. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [PUBMED:7760808, PUBMED:8990123]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||nucleic acid binding (GO:0003676)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands .
The clan contains the following 45 members:BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Previous IDs:||Aspartyl_tRNA_N; tRNA_anti;|
|Author:||Bateman A, Mian N, Finn RD|
|Number in seed:||640|
|Number in full:||22969|
|Average length of the domain:||80.20 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||12.26 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||20|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the tRNA_anti-codon domain has been found. There are 111 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...